Atomistry » Mercury » PDB 1czs-1g4o » 1dkp
Atomistry »
  Mercury »
    PDB 1czs-1g4o »
      1dkp »

Mercury in PDB 1dkp: Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge

Enzymatic activity of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge

All present enzymatic activity of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge, PDB code: 1dkp was solved by D.Lim, S.Golovan, C.W.Forsberg, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.573, 75.127, 90.393, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.7

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge (pdb code 1dkp). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge, PDB code: 1dkp:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 1dkp

Go back to Mercury Binding Sites List in 1dkp
Mercury binding site 1 out of 4 in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg500

b:34.4
occ:1.00
ND1 A:HIS113 2.6 33.2 1.0
O A:HOH613 2.8 25.7 1.0
O A:TYR289 2.9 42.9 1.0
O A:HOH820 3.1 50.3 1.0
CG A:HIS113 3.4 32.8 1.0
CB A:HIS113 3.4 28.3 1.0
CE1 A:HIS113 3.6 34.9 1.0
C A:TYR289 4.0 42.4 1.0
CA A:HIS113 4.1 27.3 1.0
O A:HOH798 4.4 34.4 1.0
CA A:GLY290 4.6 43.0 1.0
CD2 A:HIS113 4.6 36.1 1.0
NE2 A:HIS113 4.7 38.4 1.0
N A:GLY290 4.7 40.8 1.0
CG2 A:THR111 4.8 31.5 1.0
CA A:TYR289 5.0 40.5 1.0

Mercury binding site 2 out of 4 in 1dkp

Go back to Mercury Binding Sites List in 1dkp
Mercury binding site 2 out of 4 in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg501

b:37.4
occ:0.60
NE2 A:HIS282 2.6 53.3 1.0
O A:LEU293 2.7 40.9 1.0
O A:HOH866 2.8 50.6 1.0
O A:HOH865 2.9 44.8 1.0
OE1 A:GLN287 3.1 58.9 1.0
OE1 A:GLN285 3.1 70.4 1.0
CD2 A:HIS282 3.5 53.8 1.0
CG A:GLN285 3.5 66.1 1.0
C A:LEU293 3.5 41.8 1.0
CE1 A:HIS282 3.6 56.0 1.0
CD A:GLN285 3.7 70.5 1.0
CB A:LEU293 4.0 41.1 1.0
CD A:GLN287 4.2 62.4 1.0
OG1 A:THR277 4.3 46.0 1.0
N A:PRO294 4.3 41.3 1.0
CA A:LEU293 4.3 42.7 1.0
CD A:PRO294 4.4 35.0 1.0
O A:GLN285 4.5 60.7 1.0
O A:PRO283 4.5 50.7 1.0
N A:LEU293 4.6 43.8 1.0
CG A:HIS282 4.6 52.4 1.0
ND1 A:HIS282 4.6 54.7 1.0
CB A:GLN287 4.8 53.0 1.0
N A:GLN285 4.9 58.9 1.0
CG A:GLN287 4.9 60.0 1.0
CB A:GLN285 4.9 63.0 1.0

Mercury binding site 3 out of 4 in 1dkp

Go back to Mercury Binding Sites List in 1dkp
Mercury binding site 3 out of 4 in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg502

b:39.7
occ:0.26
HG A:HG503 1.7 30.7 0.1
NE2 A:HIS250 2.6 26.3 1.0
OD2 A:ASP325 2.8 25.1 1.0
NH1 A:ARG16 2.9 25.2 1.0
OE2 A:GLU219 3.0 33.9 1.0
OD1 A:ASP304 3.0 32.9 1.0
CD A:GLU219 3.2 32.4 1.0
O24 A:IHP550 3.2 41.8 0.8
CZ A:ARG16 3.2 27.1 1.0
OE1 A:GLU219 3.3 31.0 1.0
NH2 A:ARG16 3.3 25.7 1.0
CE1 A:HIS250 3.5 27.4 1.0
CD2 A:HIS250 3.6 21.6 1.0
O A:THR327 3.6 28.1 1.0
CG A:ASP325 3.6 24.7 1.0
OD1 A:ASP325 3.7 29.2 1.0
CG A:ASP304 4.0 32.3 1.0
CB A:ASP304 4.0 27.7 1.0
NE A:ARG16 4.1 23.8 1.0
OG1 A:THR327 4.2 27.7 1.0
CG A:GLU219 4.2 23.7 1.0
C A:THR327 4.5 26.0 1.0
ND1 A:HIS250 4.5 30.4 1.0
P4 A:IHP550 4.6 39.2 0.8
CG A:HIS250 4.6 27.1 1.0
CZ A:PHE254 4.8 26.1 1.0
CD A:ARG16 4.8 22.2 1.0
CB A:GLU219 4.9 23.1 1.0
O34 A:IHP550 4.9 41.7 0.8

Mercury binding site 4 out of 4 in 1dkp

Go back to Mercury Binding Sites List in 1dkp
Mercury binding site 4 out of 4 in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg503

b:30.7
occ:0.15
HG A:HG502 1.7 39.7 0.3
OG1 A:THR327 2.6 27.7 1.0
NE2 A:HIS250 2.7 26.3 1.0
OD1 A:ASP325 2.9 29.2 1.0
O A:THR327 3.0 28.1 1.0
OD2 A:ASP325 3.1 25.1 1.0
OD1 A:ASP304 3.3 32.9 1.0
CG A:ASP325 3.4 24.7 1.0
CD2 A:HIS250 3.4 21.6 1.0
CB A:ASP304 3.6 27.7 1.0
O A:HOH604 3.7 26.8 1.0
C A:THR327 3.7 26.0 1.0
CB A:THR327 3.8 25.5 1.0
NH1 A:ARG16 3.8 25.2 1.0
CG A:ASP304 3.9 32.3 1.0
CE1 A:HIS250 3.9 27.4 1.0
CA A:THR327 4.2 25.7 1.0
CZ A:ARG16 4.2 27.1 1.0
OE2 A:GLU219 4.2 33.9 1.0
CZ A:PHE254 4.3 26.1 1.0
N A:THR327 4.3 21.9 1.0
O24 A:IHP550 4.4 41.8 0.8
CE2 A:PHE254 4.4 26.1 1.0
CE1 A:PHE254 4.6 29.3 1.0
CG A:HIS250 4.6 27.1 1.0
NH2 A:ARG16 4.7 25.7 1.0
N A:PRO328 4.7 26.5 1.0
CD A:GLU219 4.7 32.4 1.0
NE A:ARG16 4.8 23.8 1.0
CD2 A:PHE254 4.8 27.6 1.0
OE1 A:GLU219 4.8 31.0 1.0
ND1 A:HIS250 4.9 30.4 1.0
CB A:ASP325 4.9 24.6 1.0
CG2 A:THR327 5.0 22.2 1.0
CD1 A:PHE254 5.0 27.3 1.0
CA A:ASP304 5.0 25.8 1.0

Reference:

D.Lim, S.Golovan, C.W.Forsberg, Z.Jia. Crystal Structures of Escherichia Coli Phytase and Its Complex with Phytate. Nat.Struct.Biol. V. 7 108 2000.
ISSN: ISSN 1072-8368
PubMed: 10655611
DOI: 10.1038/72371
Page generated: Sun Dec 13 19:02:28 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy